Bacteroides fragilis is an abundant constituent of the human gut microbiome that presumably uses cell surface and secreted molecules to colonize the host and interact with other microorganisms. Although many outer membrane proteins can be predicted from the genome sequence by bioinformatic methods, the expression of these proteins under different conditions has not been examined. Furthermore, outer membrane proteins that have unusual features and proteins that are secreted by novel mechanisms cannot be identified by in silico methods. To address these issues, we are currently analyzing the outer membrane proteome and secretome of B. fragilis using multidimensional protein identification technology (MudPIT) and other mass spectrometry-based methods.